Package 'MEDIPS' - Bioconductor
Package 'MEDIPS' - Bioconductor
Package 'MEDIPS' - Bioconductor
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4 MEDIPS.addCNV<br />
chr_lengths: Object of class "numeric" : the lengths of the chromosomes included within the<br />
MEDIPS/COUPLING SET<br />
seq_pattern: Object of class "character" : the sequence pattern (e.g. CG)<br />
genome_CF: Object of class "numeric" : the coupling factor at the genomic bins<br />
number_pattern: Object of class "numeric" : the total number of sequence pattern<br />
Methods<br />
genome_name signature(object = "COUPLINGset"): extracts the reference genome of the<br />
COUPLING SET<br />
window_size signature(object = "COUPLINGset"): extracts the window size from the window_size<br />
slot COUPLING SET<br />
chr_names signature(object = "COUPLINGset"): extracts the names of the chromosomes<br />
included within the COUPLING SET<br />
chr_lengths signature(object = "COUPLINGset"): extracts the length of the chromosomes<br />
included within the COUPLING SET<br />
seq_pattern signature(object = "COUPLINGset"): extracts the sequence pattern (e.g. CpG)<br />
genome_CF signature(object = "COUPLINGset"): extracts the coupling factor at the genomic<br />
bins<br />
number_pattern signature(object = "COUPLINGset"): extracts the total number of sequence<br />
pattern<br />
show signature(object = "COUPLINGset"): prints a summary of the COUPLING SET object<br />
content<br />
Author(s)<br />
Lukas Chavez, Matthias Lienhard, Joern Dietrich<br />
Examples<br />
showClass("COUPLINGset")<br />
MEDIPS.addCNV<br />
Function to run a copy number variation analysis.<br />
Description<br />
Function calculates a CNV analysis based on two INPUT SETs by employing the DNAcopy package.<br />
The results are attached to a provided result table.<br />
Usage<br />
MEDIPS.addCNV(ISet1, ISet2, results, cnv.Frame=1000)
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